Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/pear pear-merger-0.9.6 as wip/ pear.

[Jason Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed May 11 14:08:58 2016 -0500
Changeset:	f3eb19aadcf90e26813957508577886e064cb04f

Added Files:
	pear/DESCR
	pear/Makefile
	pear/PLIST
	pear/TODO
	pear/distinfo
	pear/patches/patch-src_reader.c

Log Message:
Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/pear
pear-merger-0.9.6 as wip/pear.

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read
merger. It is fully parallelized and can run with as low as just a few
kilobytes of memory.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=f3eb19aadcf90e26813957508577886e064cb04f

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 pear/DESCR                      |  3 +++
 pear/Makefile                   | 31 +++++++++++++++++++++++++++++++
 pear/PLIST                      |  3 +++
 pear/TODO                       |  1 +
 pear/distinfo                   |  6 ++++++
 pear/patches/patch-src_reader.c | 16 ++++++++++++++++
 6 files changed, 60 insertions(+)

diffs:
diff --git a/pear/DESCR b/pear/DESCR
new file mode 100644
index 0000000..df36aa3
--- /dev/null
+++ b/pear/DESCR
@@ -0,0 +1,3 @@
+PEAR is an ultrafast, memory-efficient and highly accurate pair-end read
+merger. It is fully parallelized and can run with as low as just a few
+kilobytes of memory.
diff --git a/pear/Makefile b/pear/Makefile
new file mode 100644
index 0000000..fff6472
--- /dev/null
+++ b/pear/Makefile
@@ -0,0 +1,31 @@
+# $NetBSD$
+#
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+DISTNAME=	pear-${PORTVERSION}-src
+PKGNAME=	pear-merger-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	http://sco.h-its.org/exelixis/web/software/pear/files/
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	http://sco.h-its.org/exelixis/web/software/pear/
+COMMENT=	Memory-efficient and highly accurate pair-end read merger
+# LICENSE=	Creative commons
+
+GNU_CONFIGURE=	yes
+
+PORTVERSION=	0.9.6
+
+INSTALLATION_DIRS=	bin ${PKGMANDIR}/man1
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/src/pear ${DESTDIR}${PREFIX}/bin/pearRM
+	${LN} ${WRKSRC}/man/pear.1 ${WRKSRC}/man/pearRM.1
+	${INSTALL_MAN} ${WRKSRC}/man/pearRM.1 \
+		${DESTDIR}${PREFIX}/${PKGMANDIR}/man1
+
+.include "../../archivers/bzip2/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/pear/PLIST b/pear/PLIST
new file mode 100644
index 0000000..e56c9e3
--- /dev/null
+++ b/pear/PLIST
@@ -0,0 +1,3 @@
+@comment $NetBSD$
+bin/pearRM
+man/man1/pearRM.1
diff --git a/pear/TODO b/pear/TODO
new file mode 100644
index 0000000..b687356
--- /dev/null
+++ b/pear/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/pear/distinfo b/pear/distinfo
new file mode 100644
index 0000000..5172dd8
--- /dev/null
+++ b/pear/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (pear-0.9.6-src.tar.gz) = 351bde183653facb9c6a4e0b7a4328a130c3b903
+RMD160 (pear-0.9.6-src.tar.gz) = 2b90f628135a9b9610eb48f7e8816dbf49092c38
+SHA512 (pear-0.9.6-src.tar.gz) = 8761426d0bb6c2b7aedde3e78858aa22e3a4fca65fa1f4712b6165497707228af60c2048eca94c9728fabf17b70748f32c08f39f832ffa36e9ab913290b73f87
+Size (pear-0.9.6-src.tar.gz) = 292790 bytes
diff --git a/pear/patches/patch-src_reader.c b/pear/patches/patch-src_reader.c
new file mode 100644
index 0000000..a169f3e
--- /dev/null
+++ b/pear/patches/patch-src_reader.c
@@ -0,0 +1,16 @@
+$NetBSD$
+
+--- src/reader.c.orig	2015-01-15 16:23:52.000000000 +0000
++++ src/reader.c
+@@ -13,6 +13,11 @@
+ #include <zlib.h>
+ #endif
+ 
++// Base zlib on NetBSD 6 lacks gzoffset()
++#ifdef __NetBSD__
++#define	gzoffset(file)	gzseek(file,0,SEEK_CUR)
++#endif
++
+ #define READ_SIZE 400
+ 
+ #define PEAR_FILETYPE_FASTQ     1 << 0